We demonstrate a novel approach to quantify the inter-particle distance in colloidal dimers using Mie scattering. The inter-particle distance is varied in a controlled way by changing the ionic strength of the solution and the magnetic attraction between the particles. The measured scaling behavior is interpreted using an energy-distance model that includes the repulsive electrostatic and attractive magnetic interactions. The center-to-center distances of particles with a 525nm radius can be determined with a root mean square accuracy of 12 nm. The data shows that the center-to-center distance is larger by 83nm compared to perfect spheres. The underlying distance offset can be attributed to repulsion by charged protrusions, caused by particle surface roughness. The measurement method accurately quanties inter-particle distances that can be used to study cluster formation and colloid aggregation in complex systems e.g. in biosensing applications.